Chromosomal-level Genome Assembly of the Endangered Golden Birdwing Butterfly Troides aeacus

Core Concepts

The first high-quality, chromosomal-level genome assembly of the golden birdwing butterfly Troides aeacus, an ecologically important and endangered species, provides a valuable resource for understanding its biology and supporting conservation efforts.

Abstract

The golden birdwing butterfly Troides aeacus is a large swallowtail butterfly widely distributed in Asia. Despite its ecological importance, the lack of genomic resources has hindered our understanding of its biology and diversity, as well as the implementation of effective conservation measures.
This study presents the first chromosomal-level genome assembly of T. aeacus, generated using a combination of PacBio SMRT and Omni-C scaffolding technologies. The assembled genome is 351 Mb in size, with 98.94% of the sequences anchored to 30 pseudo-molecules. The genome assembly has high sequence continuity, with a scaffold N50 of 12.2 Mb, and a high BUSCO score completeness of 98.9%.
The genome annotation predicted a total of 28,749 protein-coding genes. Analysis of the repetitive content revealed that LINE elements are the most abundant, followed by SINE retrotransposons and DNA transposons. Telomeric repeats were identified in 25 scaffolds, providing insights into the chromosome structure.
This high-quality genome assembly offers a significant new resource for understanding the biology of the swallowtail butterfly, as well as supporting conservation efforts for this ecologically important lepidopteran species.

Stats

A total of 27 Gb of HiFi bases were yielded with an average HiFi read length of 9,688 bp and 78X coverage.
The assembled genome is 350.66 Mb in size with 36 scaffolds, of which 30 scaffolds are of chromosome length.
The genome has a scaffold N50 value of 12.21 Mb and a BUSCO completeness of 98.9% (metazoa_odb10).
The genome size estimation is about 268.3 Mb with 2.93% nucleotide heterozygosity rate.
A total of 32,183 gene models were predicted with a BUSCO score of 86.5%.
The repetitive content of the assembled genome is 29.50%, including 5.16% unclassified elements.

Quotes

"This high-quality genome assembly offers a new and significant resource for understanding the swallowtail butterfly biology, as well as carrying out conservation measures of this ecologically important lepidopteran species."
"The assembled genome (351 Mb) contains 98.94% of the sequences anchored to 30 pseudo-molecules. The genome assembly also has high sequence continuity with scaffold length N50 = 12.2 Mb."

Key Insights Distilled From

Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860)

by Hong Kong Bi... at www.biorxiv.org 01-15-2024

https://www.biorxiv.org/content/10.1101/2024.01.13.575334v1

Deeper Inquiries

How can the genomic resources provided by this study be leveraged to support the conservation and management of the golden birdwing butterfly populations across its native range?

The genomic resources generated in this study, particularly the chromosomal-level genome assembly of the golden birdwing butterfly Troides aeacus, offer valuable insights that can significantly contribute to the conservation and management of this species across its native range.

Population Genetics: By analyzing the genetic diversity within and among populations of T. aeacus, conservationists can gain a better understanding of the species' population structure, gene flow patterns, and levels of inbreeding. This information is crucial for designing effective conservation strategies, such as identifying genetically distinct populations that may require specific conservation actions.

Identifying Adaptive Traits: Comparative genomic analyses can help identify genes associated with adaptive traits in T. aeacus, such as those related to habitat preferences, host plant interactions, and responses to environmental stressors. Understanding the genetic basis of these traits can inform conservation efforts aimed at preserving the species' ability to adapt to changing environments.

Conservation Breeding Programs: The genomic data can guide the establishment of conservation breeding programs for T. aeacus by providing information on genetic diversity, inbreeding risks, and population connectivity. Captive breeding efforts can be informed by genetic data to ensure the maintenance of genetic diversity and the preservation of adaptive potential in captive populations.

Monitoring Genetic Health: Genomic tools can be used to monitor the genetic health of wild populations of T. aeacus over time. By tracking changes in genetic diversity and detecting signs of inbreeding or genetic drift, conservationists can implement timely interventions to prevent the loss of genetic variability and maintain population viability.

Targeted Conservation Actions: The identification of genomic regions associated with important traits, such as resistance to pathogens or tolerance to climate change, can inform targeted conservation actions, such as habitat restoration, translocation of individuals, or establishment of protected areas in key habitats for the species.

What are the potential evolutionary and ecological insights that can be gained from comparative genomic analyses between the golden birdwing and other swallowtail butterfly species?

Comparative genomic analyses between the golden birdwing Troides aeacus and other swallowtail butterfly species can provide valuable insights into the evolutionary history, genetic diversity, and ecological adaptations of these butterflies.

Phylogenetic Relationships: By comparing the genomes of T. aeacus with other swallowtail species, researchers can reconstruct the evolutionary relationships among different butterfly lineages, elucidating the phylogenetic history and divergence times of these species. This information can help in understanding the evolutionary processes that have shaped the diversity of swallowtail butterflies.

Genomic Adaptations: Comparative genomics can reveal genetic adaptations that are unique to T. aeacus or shared among swallowtail species. By identifying genes under positive selection or involved in key ecological interactions (e.g., host plant utilization, mimicry, mate recognition), researchers can uncover the genetic basis of important traits that have contributed to the evolutionary success of these butterflies.

Ecological Interactions: Genomic analyses can shed light on the genetic basis of ecological interactions between T. aeacus and its host plants, predators, and competitors. Understanding the molecular mechanisms underlying these interactions can provide insights into the coevolutionary dynamics between butterflies and their biotic environment.

Diversification Patterns: Comparative genomics can help elucidate the genetic mechanisms driving diversification within the swallowtail butterfly family. By comparing genomic features such as gene content, synteny, and repetitive elements across species, researchers can identify genomic signatures associated with speciation events and adaptive radiations.

Conservation Implications: Comparative genomic analyses can inform conservation efforts by identifying genomic regions associated with adaptive traits, genetic diversity hotspots, and evolutionary constraints. This information can guide conservation prioritization, management strategies, and the development of genomic tools for monitoring population health and resilience.

Given the threats faced by the golden birdwing, such as habitat loss and overexploitation, how can the genomic data be used to develop innovative strategies for its long-term conservation?

The genomic data generated from the chromosomal-level genome assembly of the golden birdwing Troides aeacus can be instrumental in developing innovative strategies for the long-term conservation of this species in the face of threats like habitat loss and overexploitation.

Genetic Monitoring: Genomic data can be used to establish baseline genetic profiles of T. aeacus populations, allowing for ongoing monitoring of genetic diversity, population sizes, and genetic health. This information can help conservationists track the impact of habitat loss and overexploitation on the genetic viability of the species.

Adaptive Management: By identifying genetic variants associated with adaptive traits in T. aeacus, conservationists can implement adaptive management strategies to enhance the species' resilience to environmental changes. For example, assisted gene flow or selective breeding programs can be designed based on genomic data to promote adaptive evolution in response to habitat degradation.

Habitat Restoration: Genomic data can inform habitat restoration efforts by identifying genetic markers linked to habitat preferences and dispersal abilities in T. aeacus. Restoration projects can be targeted towards areas with high genetic diversity or unique genetic variants to maximize the species' chances of survival and adaptation.

Anti-Trafficking Measures: Genomic tools can be used to trace the origin of illegally traded T. aeacus individuals, helping law enforcement agencies combat wildlife trafficking. DNA fingerprinting and population genetic analyses can provide evidence to prosecute traffickers and deter the illegal trade of this protected species.

Population Connectivity: Genomic data can reveal patterns of population connectivity and gene flow in T. aeacus, guiding the design of conservation corridors and translocation programs to enhance genetic exchange between fragmented populations. Maintaining genetic connectivity is essential for the long-term viability of the species in the face of habitat fragmentation.

Community Engagement: Utilizing genomic information in conservation outreach and education programs can raise awareness about the genetic importance of T. aeacus and garner support for conservation initiatives. Engaging local communities in citizen science projects that involve genetic monitoring can foster stewardship and conservation action for the species.